Starting phenix.real_space_refine on Sun May 18 07:12:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683.map" model { file = "/net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8irr_35683/05_2025/8irr_35683_neut_trim.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 438 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 55 5.16 5 C 5259 2.51 5 N 1424 2.21 5 O 1511 1.98 5 H 8080 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 70 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16329 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 3744 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 2 Chain: "B" Number of atoms: 5108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5108 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "G" Number of atoms: 882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 882 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "N" Number of atoms: 1913 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1913 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "R" Number of atoms: 4570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 4570 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 10, 'TRANS': 271} Chain breaks: 3 Chain: "R" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 112 Unusual residues: {'CLR': 3, 'R5F': 1} Classifications: {'undetermined': 4, 'water': 2} Link IDs: {None: 5} Time building chain proxies: 7.87, per 1000 atoms: 0.48 Number of scatterers: 16329 At special positions: 0 Unit cell: (100, 106.4, 116, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 55 16.00 O 1511 8.00 N 1424 7.00 C 5259 6.00 H 8080 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.02 Simple disulfide: pdb=" SG CYS R 96 " - pdb=" SG CYS R 186 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.32 Conformation dependent library (CDL) restraints added in 1.2 seconds 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1958 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 10 sheets defined 45.3% alpha, 20.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 39 Processing helix chain 'A' and resid 52 through 56 Processing helix chain 'A' and resid 95 through 101 Processing helix chain 'A' and resid 120 through 134 Processing helix chain 'A' and resid 148 through 158 Processing helix chain 'A' and resid 162 through 167 Processing helix chain 'A' and resid 168 through 172 Processing helix chain 'A' and resid 186 through 206 removed outlier: 3.761A pdb=" N PHE A 200 " --> pdb=" O ILE A 196 " (cutoff:3.500A) Processing helix chain 'A' and resid 225 through 246 Processing helix chain 'B' and resid 4 through 26 removed outlier: 3.501A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.547A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 24 removed outlier: 3.744A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 removed outlier: 3.563A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 Processing helix chain 'N' and resid 107 through 112 removed outlier: 3.689A pdb=" N VAL N 110 " --> pdb=" O CYS N 107 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N THR N 111 " --> pdb=" O PHE N 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 22 through 51 Processing helix chain 'R' and resid 51 through 57 removed outlier: 3.762A pdb=" N ARG R 55 " --> pdb=" O PHE R 51 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LYS R 57 " --> pdb=" O HIS R 53 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 77 removed outlier: 3.829A pdb=" N PHE R 61 " --> pdb=" O LYS R 57 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE R 62 " --> pdb=" O VAL R 58 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 88 removed outlier: 3.553A pdb=" N LYS R 81 " --> pdb=" O VAL R 77 " (cutoff:3.500A) Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' Processing helix chain 'R' and resid 95 through 127 Processing helix chain 'R' and resid 127 through 135 Processing helix chain 'R' and resid 136 through 161 removed outlier: 3.599A pdb=" N SER R 155 " --> pdb=" O SER R 151 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE R 157 " --> pdb=" O LEU R 153 " (cutoff:3.500A) Proline residue: R 158 - end of helix Processing helix chain 'R' and resid 191 through 203 Processing helix chain 'R' and resid 203 through 240 Processing helix chain 'R' and resid 264 through 298 removed outlier: 3.532A pdb=" N PHE R 281 " --> pdb=" O ILE R 277 " (cutoff:3.500A) Proline residue: R 287 - end of helix removed outlier: 3.721A pdb=" N CYS R 293 " --> pdb=" O PHE R 289 " (cutoff:3.500A) Proline residue: R 296 - end of helix Processing helix chain 'R' and resid 309 through 332 removed outlier: 3.931A pdb=" N VAL R 315 " --> pdb=" O ASN R 311 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE R 316 " --> pdb=" O THR R 312 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ASN R 323 " --> pdb=" O PHE R 319 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N SER R 324 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N SER R 325 " --> pdb=" O TRP R 321 " (cutoff:3.500A) Proline residue: R 328 - end of helix Processing helix chain 'R' and resid 334 through 345 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 76 removed outlier: 9.121A pdb=" N ALA A 105 " --> pdb=" O THR A 40 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N ARG A 42 " --> pdb=" O ALA A 105 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N ILE A 107 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU A 44 " --> pdb=" O ILE A 107 " (cutoff:3.500A) removed outlier: 7.646A pdb=" N VAL A 109 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N LEU A 46 " --> pdb=" O VAL A 109 " (cutoff:3.500A) removed outlier: 8.239A pdb=" N ASP A 111 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N VAL A 142 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N HIS A 217 " --> pdb=" O VAL A 142 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N LEU A 144 " --> pdb=" O HIS A 217 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 6.697A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.484A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.366A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.767A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.606A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 189 through 192 removed outlier: 3.552A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.650A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN B 259 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.679A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'N' and resid 10 through 12 removed outlier: 6.724A pdb=" N MET N 34 " --> pdb=" O ASP N 50 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ASP N 50 " --> pdb=" O MET N 34 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) 446 hydrogen bonds defined for protein. 1260 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.70 Time building geometry restraints manager: 5.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 8045 1.13 - 1.30: 1452 1.30 - 1.47: 3227 1.47 - 1.65: 3705 1.65 - 1.82: 75 Bond restraints: 16504 Sorted by residual: bond pdb=" NH1 ARG A 191 " pdb="HH12 ARG A 191 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 PHE R 129 " pdb=" HD2 PHE R 129 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER N 63 " pdb=" H SER N 63 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N PHE N 29 " pdb=" H PHE N 29 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N GLY B 216 " pdb=" H GLY B 216 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 ... (remaining 16499 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 24460 2.15 - 4.30: 3598 4.30 - 6.45: 1179 6.45 - 8.59: 396 8.59 - 10.74: 7 Bond angle restraints: 29640 Sorted by residual: angle pdb=" N ILE B 58 " pdb=" CA ILE B 58 " pdb=" C ILE B 58 " ideal model delta sigma weight residual 109.58 100.79 8.79 1.29e+00 6.01e-01 4.64e+01 angle pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " pdb=" CG ASN B 119 " ideal model delta sigma weight residual 112.60 118.64 -6.04 1.00e+00 1.00e+00 3.64e+01 angle pdb=" N ALA B 203 " pdb=" CA ALA B 203 " pdb=" C ALA B 203 " ideal model delta sigma weight residual 109.24 119.98 -10.74 1.89e+00 2.80e-01 3.23e+01 angle pdb=" C CYS B 204 " pdb=" N ASP B 205 " pdb=" CA ASP B 205 " ideal model delta sigma weight residual 121.87 131.16 -9.29 1.64e+00 3.72e-01 3.21e+01 angle pdb=" N ALA B 60 " pdb=" CA ALA B 60 " pdb=" C ALA B 60 " ideal model delta sigma weight residual 108.42 116.77 -8.35 1.54e+00 4.22e-01 2.94e+01 ... (remaining 29635 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.41: 7176 17.41 - 34.82: 473 34.82 - 52.23: 132 52.23 - 69.64: 156 69.64 - 87.05: 10 Dihedral angle restraints: 7947 sinusoidal: 4357 harmonic: 3590 Sorted by residual: dihedral pdb=" C ASN B 119 " pdb=" N ASN B 119 " pdb=" CA ASN B 119 " pdb=" CB ASN B 119 " ideal model delta harmonic sigma weight residual -122.60 -138.21 15.61 0 2.50e+00 1.60e-01 3.90e+01 dihedral pdb=" CA MET B 61 " pdb=" C MET B 61 " pdb=" N HIS B 62 " pdb=" CA HIS B 62 " ideal model delta harmonic sigma weight residual 180.00 150.52 29.48 0 5.00e+00 4.00e-02 3.48e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 150.79 29.21 0 5.00e+00 4.00e-02 3.41e+01 ... (remaining 7944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.116: 1049 0.116 - 0.232: 221 0.232 - 0.348: 21 0.348 - 0.464: 4 0.464 - 0.580: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA ASN B 119 " pdb=" N ASN B 119 " pdb=" C ASN B 119 " pdb=" CB ASN B 119 " both_signs ideal model delta sigma weight residual False 2.51 1.93 0.58 2.00e-01 2.50e+01 8.40e+00 chirality pdb=" CA GLN B 75 " pdb=" N GLN B 75 " pdb=" C GLN B 75 " pdb=" CB GLN B 75 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.07e+00 chirality pdb=" CA ALA B 302 " pdb=" N ALA B 302 " pdb=" C ALA B 302 " pdb=" CB ALA B 302 " both_signs ideal model delta sigma weight residual False 2.48 2.10 0.38 2.00e-01 2.50e+01 3.62e+00 ... (remaining 1293 not shown) Planarity restraints: 2425 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP R 148 " 0.230 2.00e-02 2.50e+03 9.78e-02 3.82e+02 pdb=" CG TRP R 148 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP R 148 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TRP R 148 " -0.058 2.00e-02 2.50e+03 pdb=" NE1 TRP R 148 " -0.070 2.00e-02 2.50e+03 pdb=" CE2 TRP R 148 " -0.043 2.00e-02 2.50e+03 pdb=" CE3 TRP R 148 " -0.086 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 148 " 0.025 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 148 " -0.024 2.00e-02 2.50e+03 pdb=" CH2 TRP R 148 " 0.066 2.00e-02 2.50e+03 pdb=" HD1 TRP R 148 " 0.025 2.00e-02 2.50e+03 pdb=" HE1 TRP R 148 " -0.136 2.00e-02 2.50e+03 pdb=" HE3 TRP R 148 " -0.154 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 148 " 0.046 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 148 " -0.045 2.00e-02 2.50e+03 pdb=" HH2 TRP R 148 " 0.166 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 63 " 0.185 2.00e-02 2.50e+03 6.92e-02 1.92e+02 pdb=" CG TRP B 63 " -0.002 2.00e-02 2.50e+03 pdb=" CD1 TRP B 63 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TRP B 63 " -0.083 2.00e-02 2.50e+03 pdb=" NE1 TRP B 63 " -0.040 2.00e-02 2.50e+03 pdb=" CE2 TRP B 63 " -0.057 2.00e-02 2.50e+03 pdb=" CE3 TRP B 63 " -0.066 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 63 " 0.012 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 63 " -0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP B 63 " 0.039 2.00e-02 2.50e+03 pdb=" HD1 TRP B 63 " 0.027 2.00e-02 2.50e+03 pdb=" HE1 TRP B 63 " -0.055 2.00e-02 2.50e+03 pdb=" HE3 TRP B 63 " -0.102 2.00e-02 2.50e+03 pdb=" HZ2 TRP B 63 " 0.044 2.00e-02 2.50e+03 pdb=" HZ3 TRP B 63 " 0.012 2.00e-02 2.50e+03 pdb=" HH2 TRP B 63 " 0.091 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 285 " 0.072 2.00e-02 2.50e+03 6.26e-02 1.57e+02 pdb=" CG TRP R 285 " 0.079 2.00e-02 2.50e+03 pdb=" CD1 TRP R 285 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP R 285 " 0.053 2.00e-02 2.50e+03 pdb=" NE1 TRP R 285 " -0.031 2.00e-02 2.50e+03 pdb=" CE2 TRP R 285 " 0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP R 285 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 285 " 0.038 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 285 " -0.050 2.00e-02 2.50e+03 pdb=" CH2 TRP R 285 " 0.020 2.00e-02 2.50e+03 pdb=" HD1 TRP R 285 " -0.088 2.00e-02 2.50e+03 pdb=" HE1 TRP R 285 " -0.078 2.00e-02 2.50e+03 pdb=" HE3 TRP R 285 " 0.003 2.00e-02 2.50e+03 pdb=" HZ2 TRP R 285 " 0.055 2.00e-02 2.50e+03 pdb=" HZ3 TRP R 285 " -0.145 2.00e-02 2.50e+03 pdb=" HH2 TRP R 285 " 0.060 2.00e-02 2.50e+03 ... (remaining 2422 not shown) Histogram of nonbonded interaction distances: 1.39 - 2.03: 480 2.03 - 2.67: 21014 2.67 - 3.32: 49625 3.32 - 3.96: 65577 3.96 - 4.60: 96032 Nonbonded interactions: 232728 Sorted by model distance: nonbonded pdb=" HA VAL B 315 " pdb=" HG SER B 331 " model vdw 1.388 2.270 nonbonded pdb=" HG SER N 52 " pdb=" H GLN N 53 " model vdw 1.401 2.100 nonbonded pdb="HD21 ASN A 50 " pdb=" HD3 ARG A 120 " model vdw 1.462 2.270 nonbonded pdb=" HE2 HIS B 54 " pdb=" HG SER B 72 " model vdw 1.507 2.100 nonbonded pdb=" OE2 GLU B 226 " pdb=" HH TYR N 32 " model vdw 1.626 2.450 ... (remaining 232723 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.300 Extract box with map and model: 0.680 Check model and map are aligned: 0.130 Set scattering table: 0.160 Process input model: 35.040 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7873 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.012 0.070 8427 Z= 0.747 Angle : 1.804 10.742 11432 Z= 1.213 Chirality : 0.095 0.580 1296 Planarity : 0.016 0.124 1433 Dihedral : 12.313 87.049 3211 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 1.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.31 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.37 (0.24), residues: 1012 helix: 0.07 (0.22), residues: 410 sheet: 0.71 (0.37), residues: 189 loop : -0.94 (0.29), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.135 0.029 TRP R 148 HIS 0.025 0.006 HIS B 311 PHE 0.120 0.015 PHE N 68 TYR 0.076 0.015 TYR R 194 ARG 0.009 0.001 ARG A 191 Details of bonding type rmsd hydrogen bonds : bond 0.14680 ( 446) hydrogen bonds : angle 7.24966 ( 1260) SS BOND : bond 0.00803 ( 3) SS BOND : angle 2.68762 ( 6) covalent geometry : bond 0.01229 ( 8424) covalent geometry : angle 1.80322 (11426) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 1.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 15 GLU cc_start: 0.7311 (mt-10) cc_final: 0.7065 (mm-30) REVERT: A 29 GLN cc_start: 0.8237 (tp40) cc_final: 0.7980 (tp40) REVERT: A 32 LYS cc_start: 0.8256 (mtmt) cc_final: 0.7605 (mttt) REVERT: A 33 ASP cc_start: 0.7179 (m-30) cc_final: 0.6918 (m-30) REVERT: A 186 ASP cc_start: 0.6814 (t70) cc_final: 0.6450 (m-30) REVERT: B 44 GLN cc_start: 0.7138 (mm-40) cc_final: 0.6893 (mm-40) REVERT: G 14 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8178 (mmtm) REVERT: R 223 LYS cc_start: 0.8409 (mmtm) cc_final: 0.8060 (mmtm) REVERT: R 339 LYS cc_start: 0.8099 (tttm) cc_final: 0.7830 (tttp) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.5660 time to fit residues: 174.8800 Evaluate side-chains 173 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 173 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 0.9990 chunk 75 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 90 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 ASN A 149 GLN B 32 GLN B 75 GLN B 88 ASN G 18 GLN N 82 GLN N 84 ASN R 164 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.151490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.118484 restraints weight = 27172.357| |-----------------------------------------------------------------------------| r_work (start): 0.3367 rms_B_bonded: 2.15 r_work: 0.3237 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8427 Z= 0.174 Angle : 0.639 7.328 11432 Z= 0.352 Chirality : 0.042 0.144 1296 Planarity : 0.005 0.038 1433 Dihedral : 6.190 44.335 1337 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.35 % Allowed : 5.75 % Favored : 92.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.26), residues: 1012 helix: 1.31 (0.24), residues: 418 sheet: -0.17 (0.35), residues: 201 loop : -0.83 (0.31), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 80 HIS 0.005 0.001 HIS A 212 PHE 0.025 0.002 PHE R 288 TYR 0.013 0.002 TYR A 194 ARG 0.004 0.001 ARG N 67 Details of bonding type rmsd hydrogen bonds : bond 0.05410 ( 446) hydrogen bonds : angle 5.51518 ( 1260) SS BOND : bond 0.00491 ( 3) SS BOND : angle 0.85000 ( 6) covalent geometry : bond 0.00360 ( 8424) covalent geometry : angle 0.63910 (11426) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 174 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8239 (tp40) cc_final: 0.7839 (tp-100) REVERT: A 33 ASP cc_start: 0.7445 (m-30) cc_final: 0.7157 (m-30) REVERT: A 186 ASP cc_start: 0.7422 (t70) cc_final: 0.6739 (m-30) REVERT: G 14 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7943 (mtmm) REVERT: G 38 MET cc_start: 0.8195 (ttp) cc_final: 0.7949 (ttp) REVERT: R 223 LYS cc_start: 0.8484 (mmtm) cc_final: 0.8234 (mmtm) outliers start: 12 outliers final: 9 residues processed: 180 average time/residue: 0.5452 time to fit residues: 125.8957 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 156 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 82 GLN Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 277 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 12 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 92 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN ** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 84 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.149589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.116773 restraints weight = 27152.174| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.13 r_work: 0.3222 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 8427 Z= 0.160 Angle : 0.555 6.273 11432 Z= 0.306 Chirality : 0.041 0.138 1296 Planarity : 0.004 0.040 1433 Dihedral : 5.661 38.681 1337 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.35 % Allowed : 8.34 % Favored : 90.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.26), residues: 1012 helix: 1.54 (0.24), residues: 420 sheet: -0.35 (0.35), residues: 201 loop : -0.82 (0.31), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 80 HIS 0.005 0.001 HIS A 82 PHE 0.016 0.002 PHE R 288 TYR 0.013 0.001 TYR A 194 ARG 0.003 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04703 ( 446) hydrogen bonds : angle 5.12432 ( 1260) SS BOND : bond 0.00353 ( 3) SS BOND : angle 1.10266 ( 6) covalent geometry : bond 0.00337 ( 8424) covalent geometry : angle 0.55419 (11426) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8207 (tp40) cc_final: 0.7812 (tp-100) REVERT: A 33 ASP cc_start: 0.7530 (m-30) cc_final: 0.7216 (m-30) REVERT: A 173 TYR cc_start: 0.7296 (t80) cc_final: 0.7036 (t80) REVERT: A 186 ASP cc_start: 0.7322 (t70) cc_final: 0.6612 (m-30) REVERT: B 134 ARG cc_start: 0.6635 (ptm160) cc_final: 0.6398 (mmt180) REVERT: B 254 ASP cc_start: 0.8696 (t70) cc_final: 0.8492 (t0) REVERT: G 14 LYS cc_start: 0.8287 (ttmt) cc_final: 0.7920 (mtmm) REVERT: G 38 MET cc_start: 0.8213 (ttp) cc_final: 0.7982 (ttp) REVERT: N 82 GLN cc_start: 0.7243 (tp40) cc_final: 0.7041 (tp40) REVERT: R 223 LYS cc_start: 0.8452 (mmtm) cc_final: 0.8206 (mmtm) REVERT: R 324 SER cc_start: 0.8774 (m) cc_final: 0.8572 (t) outliers start: 12 outliers final: 10 residues processed: 176 average time/residue: 0.5245 time to fit residues: 119.5756 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 157 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 76 LEU Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 277 ILE Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 22 optimal weight: 9.9990 chunk 35 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 chunk 12 optimal weight: 6.9990 chunk 52 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN R 323 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.147992 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.114935 restraints weight = 27395.546| |-----------------------------------------------------------------------------| r_work (start): 0.3327 rms_B_bonded: 2.14 r_work: 0.3204 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3067 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.3552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 8427 Z= 0.179 Angle : 0.541 6.033 11432 Z= 0.296 Chirality : 0.040 0.135 1296 Planarity : 0.004 0.043 1433 Dihedral : 5.588 35.094 1337 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.59 % Allowed : 9.02 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1012 helix: 1.81 (0.24), residues: 414 sheet: -0.51 (0.35), residues: 209 loop : -0.79 (0.31), residues: 389 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.006 0.001 HIS A 82 PHE 0.015 0.002 PHE B 199 TYR 0.013 0.001 TYR A 194 ARG 0.004 0.001 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 446) hydrogen bonds : angle 4.94009 ( 1260) SS BOND : bond 0.00290 ( 3) SS BOND : angle 0.81141 ( 6) covalent geometry : bond 0.00383 ( 8424) covalent geometry : angle 0.54037 (11426) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 167 time to evaluate : 1.417 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8131 (tp40) cc_final: 0.7719 (tp-100) REVERT: A 32 LYS cc_start: 0.8372 (mtpt) cc_final: 0.7682 (mtmm) REVERT: A 33 ASP cc_start: 0.7558 (m-30) cc_final: 0.7220 (m-30) REVERT: A 186 ASP cc_start: 0.7223 (t70) cc_final: 0.6507 (m-30) REVERT: B 134 ARG cc_start: 0.6720 (ptm160) cc_final: 0.6489 (mmt180) REVERT: G 14 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7890 (mtmm) REVERT: G 21 MET cc_start: 0.8127 (ttp) cc_final: 0.7731 (tpt) REVERT: N 32 TYR cc_start: 0.8704 (m-80) cc_final: 0.8226 (m-80) REVERT: R 223 LYS cc_start: 0.8435 (mmtm) cc_final: 0.8194 (mmtm) REVERT: R 339 LYS cc_start: 0.8183 (tttm) cc_final: 0.7829 (tttp) outliers start: 23 outliers final: 18 residues processed: 181 average time/residue: 0.6008 time to fit residues: 141.5743 Evaluate side-chains 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 86 optimal weight: 0.0570 chunk 13 optimal weight: 5.9990 chunk 52 optimal weight: 5.9990 chunk 19 optimal weight: 4.9990 chunk 24 optimal weight: 10.0000 chunk 99 optimal weight: 7.9990 chunk 35 optimal weight: 6.9990 chunk 55 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 overall best weight: 3.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.146182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112838 restraints weight = 27742.266| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.16 r_work: 0.3172 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 8427 Z= 0.220 Angle : 0.560 6.188 11432 Z= 0.308 Chirality : 0.041 0.154 1296 Planarity : 0.004 0.062 1433 Dihedral : 5.742 42.261 1337 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 2.71 % Allowed : 10.82 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.26), residues: 1012 helix: 1.69 (0.24), residues: 414 sheet: -0.92 (0.34), residues: 219 loop : -0.81 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.004 0.001 HIS A 82 PHE 0.017 0.002 PHE B 199 TYR 0.013 0.002 TYR B 105 ARG 0.006 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04429 ( 446) hydrogen bonds : angle 4.96055 ( 1260) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.94159 ( 6) covalent geometry : bond 0.00479 ( 8424) covalent geometry : angle 0.55967 (11426) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8127 (tp40) cc_final: 0.7736 (tp-100) REVERT: A 32 LYS cc_start: 0.8352 (mtpt) cc_final: 0.7654 (mtmm) REVERT: A 33 ASP cc_start: 0.7616 (m-30) cc_final: 0.7252 (m-30) REVERT: A 173 TYR cc_start: 0.7464 (t80) cc_final: 0.7264 (t80) REVERT: A 186 ASP cc_start: 0.7221 (t70) cc_final: 0.6484 (m-30) REVERT: B 134 ARG cc_start: 0.6732 (ptm160) cc_final: 0.6519 (mmt180) REVERT: G 14 LYS cc_start: 0.8263 (ttmt) cc_final: 0.7851 (mtmm) REVERT: G 21 MET cc_start: 0.8128 (ttp) cc_final: 0.7732 (tpt) REVERT: N 13 GLN cc_start: 0.7710 (mp10) cc_final: 0.7460 (mm-40) REVERT: N 32 TYR cc_start: 0.8697 (m-80) cc_final: 0.8366 (m-80) REVERT: R 223 LYS cc_start: 0.8453 (mmtm) cc_final: 0.8212 (mmtm) REVERT: R 339 LYS cc_start: 0.8199 (tttm) cc_final: 0.7817 (tttp) outliers start: 24 outliers final: 19 residues processed: 169 average time/residue: 0.5432 time to fit residues: 118.7548 Evaluate side-chains 167 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 148 time to evaluate : 1.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 21 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 98 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.0060 chunk 65 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.146735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.112548 restraints weight = 27413.051| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.25 r_work: 0.3120 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2981 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.3898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8427 Z= 0.145 Angle : 0.507 5.768 11432 Z= 0.277 Chirality : 0.040 0.136 1296 Planarity : 0.004 0.047 1433 Dihedral : 5.437 45.805 1337 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 1.80 % Allowed : 12.29 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.26), residues: 1012 helix: 1.94 (0.25), residues: 413 sheet: -0.95 (0.34), residues: 217 loop : -0.72 (0.31), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS A 82 PHE 0.014 0.001 PHE B 199 TYR 0.011 0.001 TYR B 105 ARG 0.005 0.000 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04137 ( 446) hydrogen bonds : angle 4.77070 ( 1260) SS BOND : bond 0.00304 ( 3) SS BOND : angle 0.74376 ( 6) covalent geometry : bond 0.00308 ( 8424) covalent geometry : angle 0.50678 (11426) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8120 (tp40) cc_final: 0.7701 (tp-100) REVERT: A 32 LYS cc_start: 0.8284 (mtpt) cc_final: 0.7567 (mtmm) REVERT: A 33 ASP cc_start: 0.7608 (m-30) cc_final: 0.7227 (m-30) REVERT: A 186 ASP cc_start: 0.7214 (t70) cc_final: 0.6498 (m-30) REVERT: B 134 ARG cc_start: 0.6783 (ptm160) cc_final: 0.6475 (mmt180) REVERT: G 14 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7805 (mtmm) REVERT: G 21 MET cc_start: 0.8115 (ttp) cc_final: 0.7697 (tpt) REVERT: N 13 GLN cc_start: 0.7599 (mp10) cc_final: 0.7309 (mm-40) REVERT: N 89 GLU cc_start: 0.7783 (tt0) cc_final: 0.7570 (pt0) REVERT: R 223 LYS cc_start: 0.8410 (mmtm) cc_final: 0.8161 (mmtm) REVERT: R 339 LYS cc_start: 0.8145 (tttm) cc_final: 0.7767 (tttp) outliers start: 16 outliers final: 14 residues processed: 165 average time/residue: 0.5966 time to fit residues: 126.0935 Evaluate side-chains 164 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 150 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 24 optimal weight: 9.9990 chunk 12 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 18 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 50 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.143709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.109135 restraints weight = 27773.016| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.25 r_work: 0.3068 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.4018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 8427 Z= 0.247 Angle : 0.566 6.362 11432 Z= 0.312 Chirality : 0.042 0.153 1296 Planarity : 0.004 0.051 1433 Dihedral : 5.923 56.458 1337 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.04 % Allowed : 11.84 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.27), residues: 1012 helix: 1.72 (0.25), residues: 413 sheet: -1.18 (0.34), residues: 221 loop : -0.65 (0.32), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 96 HIS 0.004 0.001 HIS A 212 PHE 0.016 0.002 PHE B 199 TYR 0.014 0.002 TYR B 105 ARG 0.004 0.001 ARG A 172 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 446) hydrogen bonds : angle 4.93357 ( 1260) SS BOND : bond 0.00384 ( 3) SS BOND : angle 0.94202 ( 6) covalent geometry : bond 0.00543 ( 8424) covalent geometry : angle 0.56588 (11426) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8101 (tp40) cc_final: 0.7693 (tp-100) REVERT: A 32 LYS cc_start: 0.8262 (mtpt) cc_final: 0.7561 (mtmm) REVERT: A 33 ASP cc_start: 0.7709 (m-30) cc_final: 0.7319 (m-30) REVERT: A 78 LYS cc_start: 0.8735 (mttt) cc_final: 0.8238 (mttt) REVERT: A 186 ASP cc_start: 0.7211 (t70) cc_final: 0.6483 (m-30) REVERT: B 17 GLN cc_start: 0.7479 (tm-30) cc_final: 0.7221 (tm-30) REVERT: B 134 ARG cc_start: 0.6888 (ptm160) cc_final: 0.6523 (mmt180) REVERT: G 14 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7924 (mmmt) REVERT: G 21 MET cc_start: 0.8142 (ttp) cc_final: 0.7713 (tpt) REVERT: N 13 GLN cc_start: 0.7602 (mp10) cc_final: 0.7287 (mm-40) REVERT: R 223 LYS cc_start: 0.8444 (mmtm) cc_final: 0.8193 (mmtm) REVERT: R 339 LYS cc_start: 0.8171 (tttm) cc_final: 0.7895 (tttp) outliers start: 27 outliers final: 24 residues processed: 169 average time/residue: 0.5508 time to fit residues: 119.6731 Evaluate side-chains 168 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 1.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain N residue 34 MET Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 116 VAL Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 268 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 79 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 56 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 57 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.145884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.111188 restraints weight = 27512.306| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.28 r_work: 0.3112 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8427 Z= 0.144 Angle : 0.502 5.934 11432 Z= 0.276 Chirality : 0.040 0.138 1296 Planarity : 0.004 0.062 1433 Dihedral : 5.571 59.588 1337 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.03 % Allowed : 12.63 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.27), residues: 1012 helix: 1.98 (0.25), residues: 413 sheet: -1.12 (0.33), residues: 217 loop : -0.61 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 96 HIS 0.003 0.001 HIS A 82 PHE 0.020 0.001 PHE R 95 TYR 0.011 0.001 TYR B 105 ARG 0.009 0.000 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04084 ( 446) hydrogen bonds : angle 4.76751 ( 1260) SS BOND : bond 0.00292 ( 3) SS BOND : angle 0.76939 ( 6) covalent geometry : bond 0.00303 ( 8424) covalent geometry : angle 0.50225 (11426) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8058 (tp40) cc_final: 0.7692 (tp-100) REVERT: A 32 LYS cc_start: 0.8232 (mtpt) cc_final: 0.7512 (mtmm) REVERT: A 33 ASP cc_start: 0.7670 (m-30) cc_final: 0.7279 (m-30) REVERT: A 78 LYS cc_start: 0.8696 (mttt) cc_final: 0.8184 (mttt) REVERT: A 186 ASP cc_start: 0.7157 (t70) cc_final: 0.6416 (m-30) REVERT: B 134 ARG cc_start: 0.6825 (ptm160) cc_final: 0.6466 (mmt180) REVERT: G 14 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7919 (mmmt) REVERT: G 21 MET cc_start: 0.8140 (ttp) cc_final: 0.7690 (tpt) REVERT: N 13 GLN cc_start: 0.7609 (mp10) cc_final: 0.7268 (mm-40) REVERT: R 223 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8158 (mmtm) REVERT: R 339 LYS cc_start: 0.8160 (tttm) cc_final: 0.7774 (tttp) outliers start: 18 outliers final: 17 residues processed: 168 average time/residue: 0.5644 time to fit residues: 122.0414 Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 148 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 93 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 60 optimal weight: 8.9990 chunk 3 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.147645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.113266 restraints weight = 27300.938| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.27 r_work: 0.3175 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.4186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8427 Z= 0.155 Angle : 0.502 5.871 11432 Z= 0.276 Chirality : 0.040 0.141 1296 Planarity : 0.004 0.048 1433 Dihedral : 5.507 55.307 1337 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 2.37 % Allowed : 12.18 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.27), residues: 1012 helix: 2.08 (0.25), residues: 413 sheet: -1.12 (0.33), residues: 217 loop : -0.59 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 82 PHE 0.018 0.001 PHE R 95 TYR 0.011 0.001 TYR B 105 ARG 0.007 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04051 ( 446) hydrogen bonds : angle 4.73614 ( 1260) SS BOND : bond 0.00285 ( 3) SS BOND : angle 0.83716 ( 6) covalent geometry : bond 0.00331 ( 8424) covalent geometry : angle 0.50203 (11426) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 153 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8037 (tp40) cc_final: 0.7628 (tp-100) REVERT: A 32 LYS cc_start: 0.8238 (mtpt) cc_final: 0.7512 (mtmm) REVERT: A 33 ASP cc_start: 0.7659 (m-30) cc_final: 0.7253 (m-30) REVERT: A 78 LYS cc_start: 0.8682 (mttt) cc_final: 0.8175 (mttt) REVERT: A 186 ASP cc_start: 0.7164 (t70) cc_final: 0.6474 (m-30) REVERT: B 134 ARG cc_start: 0.6840 (ptm160) cc_final: 0.6479 (mmt180) REVERT: G 14 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7935 (mmmt) REVERT: G 21 MET cc_start: 0.8135 (ttp) cc_final: 0.7675 (tpt) REVERT: N 13 GLN cc_start: 0.7618 (mp10) cc_final: 0.7280 (mm-40) REVERT: R 223 LYS cc_start: 0.8408 (mmtm) cc_final: 0.8168 (mmtm) REVERT: R 339 LYS cc_start: 0.8160 (tttm) cc_final: 0.7874 (tttp) outliers start: 21 outliers final: 20 residues processed: 168 average time/residue: 0.5677 time to fit residues: 124.5289 Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 150 time to evaluate : 1.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 46 GLU Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 120 ASP Chi-restraints excluded: chain R residue 126 SER Chi-restraints excluded: chain R residue 149 THR Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Chi-restraints excluded: chain R residue 268 THR Chi-restraints excluded: chain R residue 333 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 74 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 38 optimal weight: 2.9990 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN N 35 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.148324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.114201 restraints weight = 27240.471| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 2.25 r_work: 0.3142 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3004 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.4270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 8427 Z= 0.111 Angle : 0.473 5.430 11432 Z= 0.258 Chirality : 0.039 0.139 1296 Planarity : 0.005 0.113 1433 Dihedral : 5.240 53.037 1337 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.80 % Allowed : 12.85 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.27), residues: 1012 helix: 2.33 (0.26), residues: 413 sheet: -0.94 (0.34), residues: 213 loop : -0.64 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 82 PHE 0.018 0.001 PHE R 95 TYR 0.010 0.001 TYR B 105 ARG 0.016 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.03840 ( 446) hydrogen bonds : angle 4.58366 ( 1260) SS BOND : bond 0.00213 ( 3) SS BOND : angle 0.75618 ( 6) covalent geometry : bond 0.00229 ( 8424) covalent geometry : angle 0.47300 (11426) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2024 Ramachandran restraints generated. 1012 Oldfield, 0 Emsley, 1012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 159 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8015 (tp40) cc_final: 0.7649 (tp-100) REVERT: A 32 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7468 (mtmm) REVERT: A 33 ASP cc_start: 0.7673 (m-30) cc_final: 0.7257 (m-30) REVERT: A 78 LYS cc_start: 0.8695 (mttt) cc_final: 0.8171 (mttt) REVERT: A 186 ASP cc_start: 0.7123 (t70) cc_final: 0.6448 (m-30) REVERT: B 134 ARG cc_start: 0.6801 (ptm160) cc_final: 0.6467 (mmt180) REVERT: B 150 ARG cc_start: 0.8787 (mpt180) cc_final: 0.8415 (mpt180) REVERT: B 214 ARG cc_start: 0.6844 (mtm110) cc_final: 0.6632 (mtm110) REVERT: G 14 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7900 (mmmt) REVERT: G 21 MET cc_start: 0.8089 (ttp) cc_final: 0.7631 (tpt) REVERT: N 13 GLN cc_start: 0.7588 (mp10) cc_final: 0.7226 (mm-40) REVERT: R 223 LYS cc_start: 0.8382 (mmtm) cc_final: 0.8142 (mmtm) REVERT: R 339 LYS cc_start: 0.8142 (tttm) cc_final: 0.7756 (tttp) outliers start: 16 outliers final: 14 residues processed: 170 average time/residue: 0.5689 time to fit residues: 123.1433 Evaluate side-chains 170 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 156 time to evaluate : 1.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 LEU Chi-restraints excluded: chain A residue 150 ASP Chi-restraints excluded: chain A residue 247 GLU Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 119 ASN Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 205 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain N residue 71 SER Chi-restraints excluded: chain N residue 96 CYS Chi-restraints excluded: chain R residue 38 LEU Chi-restraints excluded: chain R residue 201 ILE Chi-restraints excluded: chain R residue 207 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 9 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 68 optimal weight: 0.7980 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.147151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.112947 restraints weight = 27244.642| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.24 r_work: 0.3125 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2988 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2988 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8427 Z= 0.142 Angle : 0.482 5.643 11432 Z= 0.265 Chirality : 0.039 0.137 1296 Planarity : 0.004 0.047 1433 Dihedral : 5.277 47.468 1337 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.14 % Allowed : 12.40 % Favored : 85.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.27), residues: 1012 helix: 2.33 (0.25), residues: 413 sheet: -1.08 (0.33), residues: 218 loop : -0.56 (0.33), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 96 HIS 0.003 0.001 HIS A 82 PHE 0.016 0.001 PHE R 95 TYR 0.011 0.001 TYR A 194 ARG 0.005 0.000 ARG B 214 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 446) hydrogen bonds : angle 4.61766 ( 1260) SS BOND : bond 0.00221 ( 3) SS BOND : angle 0.76958 ( 6) covalent geometry : bond 0.00304 ( 8424) covalent geometry : angle 0.48205 (11426) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8819.89 seconds wall clock time: 151 minutes 38.56 seconds (9098.56 seconds total)